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Bioinformatics. 2013 Mar 1;29(5):658-60. doi: 10.1093/bioinformatics/btt008. Epub 2013 Jan 10.

CePa: an R package for finding significant pathways weighted by multiple network centralities.

Author information

  • 1The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Science, Department of Physics, Nanjing University, Nanjing 210093, China.

Abstract

SUMMARY:

CePa is an R package aiming to find significant pathways through network topology information. The package has several advantages compared with current pathway enrichment tools. First, pathway node instead of single gene is taken as the basic unit when analysing networks to meet the fact that genes must be constructed into complexes to hold normal functions. Second, multiple network centralities are applied simultaneously to measure importance of nodes from different aspects to make a full view on the biological system. CePa extends standard pathway enrichment methods, which include both over-representation analysis procedure and gene-set analysis procedure. CePa has been evaluated with high performance on real-world data, and it can provide more information directly related to current biological problems.

AVAILABILITY:

CePa is available at the Comprehensive R Archive Network (CRAN): http://cran.r-project.org/web/packages/CePa/

PMID:
23314125
DOI:
10.1093/bioinformatics/btt008
[PubMed - indexed for MEDLINE]
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